rs7780294

Variant names:

• chr7-128736608-C-T
• rs7780294

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.107 in 152,190 control chromosomes in the GnomAD database, including 1,918 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1918 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16283 AN: 152072 Hom.: 1916 Cov.: 33

Gnomad AFR AF: 0.0424

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.0986

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.107 AC: 16296 AN: 152190 Hom.: 1918 Cov.: 33 AF XY: 0.114 AC XY: 8513 AN XY: 74416

African (AFR) AF: 0.0423 AC: 1757 AN: 41544

American (AMR) AF: 0.250 AC: 3814 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3468

East Asian (EAS) AF: 0.586 AC: 3027 AN: 5168

South Asian (SAS) AF: 0.184 AC: 885 AN: 4818

European-Finnish (FIN) AF: 0.107 AC: 1136 AN: 10604

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0762 AC: 5182 AN: 67986

Other (OTH) AF: 0.0999 AC: 211 AN: 2112

Alfa AF: 0.0912 Hom.: 1788

Bravo AF: 0.119

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7780294; hg19: chr7-128376662;